Take some time off.Have you seen a physio or specialist yet to actually tell you whats wrong?.I had a patella problem which gave me similar problems... exagerated by riding mtbs a lot and trying to ride every obstacle which meant falling off too much . In the end I just took 6 weeks off the bike. When I got back on I took it easy building back up. Muscles grow strong much quicker than knees... even now knees give me problems only if I try and up the kms too quickly. I push big gears everywhere no issues... just have to give my knees time to build up especially after winter when suddenly the kms double or triple.

It was totally doing my head in that I wasn't getting discomfort/pain when on my trainer or putting in a hard effort, and then the other day while trying to take it easy I looked down and noticed that when my heel was going through 6 o'clock I was dropping my heel ALOT, so I thought maybe if I concentrated on keeping my heel flat that I wouldn't get the pain, so after a few days off to get my knee back to normal I went out and concentrated on not dropping my heel and success I had no discomfort at all, so to be sure I hammered myself as hard as I could to try and stress my knee and not even a niggle. Then after a confirmation ride just then I think I have beat it.

What I think was happening was that in an attempt to ride 'easy' I was getting really lazy with my pedalling by concentrating more on relaxing my leg muscles more then technique.

Of course there was more to it earlier when I tried mucking around with my setup to much.

So by dropping your heel too much your effectively making your seat height a lot higher which is bad.

Prior to our holiday in Yurp, I had been doing plenty of hills and had quite a bit of pain across the patella. So when I hired an S-Works Roubaix in Grenoble, I was very pleasantly surprised to discover no knee pain. The answer was obvious; a considerably higher saddle. The shop guy set the height by looking at me. I went along with it thinking I would lower it later. Same thing happened in Bourg d'Oisins.

I had always gone with the 30% bend rule. But now I have much less and no knee troubles.

It’s more like our thoughts are thinking us than we are thinking them.